All next-generation sequencing (NGS) platforms provide exciting opportunities for the sequencing of amplicons. In contrast to traditional Sanger sequencing, NGS technologies allow a variety of samples to be analyzed at in parallel. This eliminates the need for isolating or culturing a single sample prior to sequencing. Instead, diverse samples can be analyzed in a “massively parallel” (to use a common NGS synonym) manner to gain insight into heterogeneous starting material.
The field of metagenomics is an application that makes regular use of amplicon NGS. “Metagenomics” refers to the study of genetic material that comes directly from environmental samples. This is in contrast to more tradition, culture-based laboratory methods that required isolation and growth of a specific organism prior to analysis. NGS platforms allow DNA isolated directly from environmental samples to be analyzed to determine their composition.
Specifically, bacterial, eukaryotic, and fungal organisms can be identified to the genus level using targeted sequencing of the 16S, 18S, and ITS regions, respectively. Within both bacterial and eukaryotic genomes there exist highly conserved regions that code for ribosomal RNA (rRNA). In bacteria this is the “16S” region and in eukaryotes this is the “18S” region. Within fungal genomes the internal transcribed spacer (ITS) region is used for the same purpose. These regions are targeted using PCR-based amplification to produce sequencing libraries that, when analyzed, can provide information about the presence and relative abundance of various organisms in a given sample.
For standard 16S/18S/ITS services, data is delivered as both FASTQ.gz and OTU analysis files through Globus Connect or a direct transfer into your Amazon Web Services (AWS) S3 account, if available.